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BMR. Metatranscriptome sequencing from Tara Oceans Polar Circle RNA samples corresponding to size fractions for prokaryotes.

ABSTRACT: Metatranscriptome sequencing from Tara Oceans Polar Circle RNA samples corresponding to size fractions for prokaryotes.

PROVIDER: PRJEB9741 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3586680_1.fastq.gz	Fastqsanger.gz
	ERR3586680_2.fastq.gz	Fastqsanger.gz
	ERR3586690_1.fastq.gz	Fastqsanger.gz
	ERR3586690_2.fastq.gz	Fastqsanger.gz
	ERR3586700_1.fastq.gz	Fastqsanger.gz

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BII. Metatranscriptome sequencing from Tara Oceans Polar Circle samples corresponding to size fractions for protists.

Project description:Metatranscriptome sequencing from Tara Oceans Polar Circle samples corresponding to size fractions for protists.

| PRJEB9738 | ENA

BIK. Metatranscriptome sequencing from Tara Oceans Polar Circle samples corresponding to size fractions for protists.

Project description:Metatranscriptome sequencing from Tara Oceans Polar Circle samples corresponding to size fractions for protists.

| PRJEB9739 | ENA

BHQ. Amplicon sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

Project description:Amplicon sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

| PRJEB9737 | ENA

BHN - Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

Project description:Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

| PRJEB9691 | ENA

BMI. Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for prokaryotes.

Project description:Shotgun Sequencing of Tara Oceans Polar Cicle DNA samples corresponding to size fractions for prokaryotes.

| PRJEB9740 | ENA

BNA. Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for small DNA viruses.

Project description:Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for small DNA viruses.

| PRJEB9742 | ENA

18S rDNA miTags information for Tara Oceans Expedition (2009-2013), including the Tara Polar Circle Expedition (2013)

Project description: Not available

| S-BSST762 | biostudies-other

TARA Oceans Viral Proteins - Illuminating structural proteins in viral "dark matter" with metaproteomics

Project description:A grand challenge in biology is the lack of annotation for much of global sequence space. In particular, while microbes and their viruses are critical to Earth System functioning, surveys of their communities in nature routinely return genes of unknown function, particularly for viruses. This hampers understanding and predictive capability, and reflects a number of database limitations. Here we apply high-resolution environmental metaproteomics to 4 purified viral concentrates from the Tara Oceans Expedition to identify in situ proteins extracted from uncultivated viral particles. Using matched metagenomic databases, we identified 1875 proteins belonging to 549 non-redundant protein clusters that are predominantly of unknown function. These data help identify function for structure-associated proteins in known abundant tailed viruses (e.g., pelagiphages and cyanophages) and validate newly-identified uncultured viral sequences linked to abundant novel hosts. One protein cluster alone comprised 22% of the identified structure-associated proteins, with ~46% of the observed spectra. Structural modeling of this highly abundant viral protein cluster indicates its likely role as a novel, previously unknown capsid. Together these analyses provide much-needed, culture-independent structure-associated protein annotations critical for identifying viral signals across diverse datasets to better elucidate viral roles in nature.

2016-02-25 | PXD000938 | Pride

DNA Microarray of B16F10 cells treated with or without 25 micromolar of tara tannin

Project description:The experiment was designed to determine the global gene expression changes in B16F10 cells as a result of treatment with 25 micromolar of tara tannin

2020-02-07 | E-MTAB-7227 | biostudies-arrayexpress

Known phyla dominate the Tara Oceans RNA virome.

Project description:A recent study proposed five new RNA virus phyla, two of which, 'Taraviricota' and 'Arctiviricota', were stated to be 'dominant in the oceans'. However, the study's assignments classify 28,353 putative RdRp-containing contigs to known phyla but only 886 (2.8%) to the five proposed new phyla combined. I re-mapped the reads to the contigs, finding that known phyla also account for a large majority (93.8%) of reads according to the study's classifications, and that contigs originally assigned to 'Arctiviricota' accounted for only a tiny fraction (0.01%) of reads from Arctic Ocean samples. Performing my own virus identification and classifications, I found that 99.95 per cent of reads could be assigned to known phyla. The most abundant species was Beihai picorna-like virus 34 (15% of reads), and the most abundant order-like cluster was classified as Picornavirales (45% of reads). Sequences in the claimed new phylum 'Pomiviricota' were placed inside a phylogenetic tree for established order Durnavirales with 100 per cent confidence. Moreover, two contigs assigned to the proposed phylum 'Taraviricota' were found to have high-identity alignments to dinoflagellate proteins, tentatively identifying this group of RdRp-like sequences as deriving from non-viral transcripts. Together, these results comprehensively contradict the claim that new phyla dominate the data.

| S-EPMC10649353 | biostudies-literature

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